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<h1>Rows filter</h1>

<h2>Description</h2>

<p>
    This module deletes all rows in a selected peak list that do not meet the requirements defined by the user. These
    requirements can be the minimum number of peaks in the row, the minimum number of peaks in an isotope pattern, peak
    duration or a m/z vs retention time window. When an aligned peak list, i.e. multiple peaks per row, is filtered then
    the average of each row's peak duration, m/z and retention time values are used to filter the row.
</p>

<h4>Method parameters</h4>
<dl>
    <dt>Name suffix</dt>
    <dd>This is the suffix used to identify the new filtered peak list in Peak list frame of the desktop.</dd>

    <dt>Minimum peaks in a row</dt>
    <dd>Minimum number of peaks in a row required to not remove it.</dd>

    <dt>Minimum peaks in an isotope pattern</dt>
    <dd>Minimum number of peaks in a row's isotope pattern required to not remove it.</dd>

    <dt>m/z range</dt>
    <dd>Range of acceptable (average) m/z values in a row required to not remove it.</dd>

    <dt>Retention time range</dt>
    <dd>Range of acceptable (average) retention times in a row required to not remove it.</dd>

    <dt>Peak duration range</dt>
    <dd>Range of acceptable (average) peak durations in a row required not to remove it.</dd>

	<dt>Chromatographic FWHM</dt>
    <dd>Range of acceptable FWHM in a row required not to remove it.</dd>

	<dt>Charge</dt>
    <dd>Range of Charge in a row required not to remove it. Please run isotopic peaks grouper first</dd>

	<dt>Kendrick mass defect</dt>
    <dd>Filter features in a Kendrick mass defect range. For more details see Kendrick mass defect setup.</dd>

    <dt>Filtering by groups</dt>
    <dd>If the checkbox is selected samples will be separated by groups before filtering the peaks and the same filtering criteria will be applied for each group.</dd>

    <dt>Parameter</dt>
    <dd>Paremeter defining the group of each sample. They have to be defined by the user using "Project-> Set sample parameters.." module.</dd>

    <dt>Only identified?</dt>
    <dd>If the checkbox is selected, only identified rows will be retained.</dd>
    
    <dt>Text in identity</dt>
    <dd>Only rows that contain this text in their peak identity field will be retained.</dd>
    
    <dt>Text in comment</dt>
    <dd>Only rows that contain this text in their comment field will be retained.</dd>

    <dt>Remove source peak list after filtering</dt>
    <dd>If the checkbox is selected, the source peak list will be removed and the filtered version remains.</dd>
</dl>

<h4>Kendrick mass defect setup</h4>
<dl>
	<dt>Kendrick mass defect</dt>
    <dd>Set Kendrick mass defect range</dd>
    
    <dt>Kendrick mass base</dt>
    <dd>Enter molecular formula of the repeating unit used as Kendrick mass base</dd>
    
    <dt>Shift</dt>
    <dd>Set shift value</dd>
    
    <dt>Charge</dt>
    <dd>Set charge value</dd>
    
    <dt>Divisor</dt>
    <dd>Set divisor value</dd>

	<dt>Use remainder of Kendrick mass</dt>
    <dd>Select check box to use RKM instead if KMD</dd>
    
    <dt>All parameters can be derived from the Kendrick mass plot visualizer to e.g. isolate all features of an observed cluster (see figure)</dt>

	<p>
	<img src="Kendrick_Filtering_Approach_Help.png">
	</p>

</dl>
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